PDA

View Full Version : Metagenomics

  1. PubMed: Profiling model T cell metagenomes with short reads.
  2. public database for metagenomic sequences
  3. Antarctica metagenomics research
  4. PubMed: Comparative day/night metatranscriptomic analysis of microbial communities in
  5. PubMed: Metagenomic analyses of viruses in the stool of children with acute flaccid p
  6. PubMed: Analyzing Gene Expression from Marine Microbial Communities using Environment
  7. PubMed: Methods for comparative metagenomics
  8. PubMed: Metagenomic signatures of 86 microbial and viral metagenomes.
  9. function/abundance prediction from reads
  10. PubMed: Suppression Subtractive Hybridisation for Metagenomic Subsampling
  11. TerraGenome Consortium
  12. NIH Awards $42 Million to Human Microbiome Projects
  13. PubMed: Exploring the oral bacterial flora: current status and future directions.
  14. PubMed: Microbial community structure in the North Pacific ocean.
  15. step by step for rarefaction calculation
  16. Rarefaction distance explanation
  17. Assembly of short reads in Metagenomic studies
  18. filtering samples
  19. Mapping against multiple sequences
  20. Illumina Metagenomics data
  21. Meta assembly
  22. 454 metagenmic data assembly
  23. Rapid Identification of Microorganisms in Solexa samples
  24. % identity cutoff
  25. Sample/library prep of DNA and RNA in a metagenomic sample
  26. Tools for Phylogenetic Trees
  27. Comparing shotgun metagenomic reads: 454 vs HiSeq
  28. metagenomics pcr in triplicate-why?
  29. Normalization of 16S PCR products
  30. sanger end-seuqencing of metagenomic fosmid library
  31. Meta-Velvet
  32. k-range in Meta-IDBA
  33. best 16s region to amplify with NGS ?
  34. the review of metagenomics assembly
  35. Publicly available Illumina metagenomes
  36. MIRA assembler for metagenomics
  37. SOlid &&&& Metagenomics
  38. MetaCV: a composition-based algorithm to classify metagenomic reads and function
  39. 16S metagenomics, how much data needed?
  40. Metagenomics analysis with CLOTU: problems with input data
  41. 454 vs MiSeq - Need to optimize time/cost for 16s analysis of 300 Stool Samples/month
  42. Tool to identify 16s rRNA fragments in raw data
  43. Quantitative 16S profiling with multiple 16S genes per genome
  44. How deep to sequence?
  45. how to deal with 16S rDNA data form Illumina
  46. analyze 16S metagenomic 200bp data to species level
  47. 16S rDNA sequencing
  48. Who uses a MiSeq for 16S data?
  49. Removing Chimeric sequences from Metagenomics samples
  50. Species abundance and rarefaction in metagenomics data
  51. Pulling bacterial and fungal seq apart
  52. Help/advise to NGS virgin....
  53. V4 region primers
  54. Metagenome assembly
  55. Assemblers
  56. Examination of PCR biases in 16S experiments.
  57. Mg-rast --> megan
  58. QIIME constraints and time to run for 16S Illumina
  59. Differential gene expression on metatranscriptome data
  60. survery: what assembler, gene prediction and gene annotation softwares do you use?
  61. 18S profiling primers
  62. fungal ITS profiling primers and 500bp Ion Torrent amplicon sequencing
  63. Sequencing 400bp 16s Amplicons on the PGM
  64. Sample collection for metranscriptomic sequencing
  65. Taxonomic assignment discrepancies between SILVA and GenBank databases
  66. Denoising Illumina reads
  67. Fungal ITS amplicon sequencing (NexteraXT vs TruSeq Custom Amplicon)
  68. Silva database
  69. Sequencing for enzyme discovery - Miseq or 454?
  70. Tophat for metagenomes?
  71. Depth & Length for individual genome reconstructrion
  72. chimera - uchime
  73. Megan for contig or gene classification
  74. metagenomics databases and summary
  75. Advies on tool selection
  76. MG-RAST - remove or retain non-overlapping paired-end reads
  77. 454 16S data from QIIME - what next?
  78. Polymerase of choice for generating 16S amplicons?
  79. Genome extraction from metagenomes
  80. demultiplexing data
  81. mothur extract the .flow data from sff file
  82. how to make a matrix of OTU abundance in each sample
  83. Organism promoting for Drought Resistant
  84. Metagenomics/Metatrancriptomics Sequencing
  85. assemble conitgs in metagenomics
  86. HUMAnN for non-HMP?
  87. Best way to search for gene homologue in metagenomic dataset
  88. Not sure which questions to be asking, or how to answer them (metagenome, metabolism)
  89. Best approach to analyze taxonomic profiling of metagenomes from environmental sample
  90. Using MetaVelvet, what hardware requirements?
  91. Bacterial species definition / OTUs
  92. Which software could be suitable for different cutoff value?
  93. How to use QIIME process MiSeq 16s data?
  94. Metamos help request
  95. Hai, I need clear protocol for DNA Barcoding in bacteria
  96. How to install qiime?
  97. MetaVelvet not running
  98. Can I combine 16S and 18S rRNA in one sequencing run?
  99. how to get gene abundance
  100. simulate metagenomic reads
  101. How do I assemble long and short contigs togeather?
  102. COG database
  103. the weighted UniFrac distances are bigger than one is normal ？
  104. Metatranscriptomics and residual human sequences
  105. Does anyone have a recommendations for graduate-level course on metagenomics?
  106. Best platform for metagenomics?
  107. Illumina 16S libs - tech & QC questions about construction and data comparison
  108. Species level identification in oral microbiome samples?
  109. Best classifier for viral reads--PhyloSift? BLAST? Others?
  110. OTU picking
  111. BLAST comparison of 16S rRNA against the SILVA database
  112. Fungal ITS sequencing Illumina
  113. Scaffolding or not?
  114. Downloading metagenomes from ncbi from terminal
  115. Considerations for a pilot study: HiSeq SR100 vs. MiSeq PE300
  116. Best 16S region for 300PE Miseq
  117. Need help to prepare sample for pyrosequencing
  118. App 16S metagenomics basespace illumina- rarefaction curves
  119. reps and analysis
  120. NORMALIZED tetranucleotides frequency
  121. Tool for viral metagenome assembly with extremely low coverage?
  122. Resequencing the same Illumina library several times
  123. Functional annotation
  124. Visualizing number of hits on KEGG map
  125. Amount of data for metagenomic analysis
  126. How to visualize microbiome datasets ?
  127. MiSeq v2 cartridges for metagenomics
  128. Minimum quantity of DNA per sample to pool?
  129. ngs tools and database
  130. Theoretical Distribution_GC Distribution_FastQC_Metagenomic Data
  131. 16S gene genomic coordinates?
  132. Free alternative to KEGG
  133. Comparing metagenomes produces with different sequencing technologies
  134. Bad assembly or bad sequence data?
  135. filtering out human contaminants
  136. seek help about UniFrac.zip
  137. Comparing OTUs from different V regions?
  138. MEGAN and blast against NR
  139. Illumina bacterial metagenomics
  140. MiSeq Reporter Metagenomics Workflow
  141. Illumina MiSeq 16S run quality
  142. Is dereplication necessary?
  143. Mismatch between PE reads
  144. beta diversity depth
  145. Understanding 16s RNA reads
  146. Recommended output or reads for 16s metagenomic
  147. high number of denovo OTU
  148. shotgun metagenomic sequencing coverage
  149. Pathogen and Probiotics database of 16S rRNA
  150. How much data should I generate for metagenomics/metatranscriptomics?
  151. Two band/peak corresponding to 400bp for V4 region
  152. Human contaminants in viral metagenome
  153. Hello All.I have annotated my metagenomic dataset using MG-RAST and now want to gener
  154. Redundancy analysis (RDA) heatmap for 16s NGS results
  155. Data I can't understand
  156. 1st metagenomic experiment
  157. Metagenomics, How much Ntd data is generated per sample in different NGS platforms.
  158. Extracting and scaffolding microbial genomes from complex communities
  159. Making a in silico mock community
  160. Many homopolymeric reads
  161. Associate gene names to respective abbreviations
  162. Paired-read analysis in MEGAN
  163. How To Run 'Merge' in the Wonderful New checkM Package
  164. What's the best way to identify the taxonomy of assembled genomes?
  165. Viral metagenomics sample with a high concentration of bacteria
  166. Controls to Consider for Metagenomics Project
  167. Experimental design
  168. Scaffolding tools for metagenomics ???
  169. MG-RAST - Alignment parameters of their process statistics?
  170. Megan attibutes file format
  171. modify megan5 taxonomy paths output
  172. Assigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?
  173. MEGAN: impact of max number of hits in read annotation
  174. Using CLARK and EBI for metagenomes
  175. 16S vs shotgun
  176. Graphic Tools for Taxonomic Assignments
  177. shell script for concatenating fastq files
  178. sequencing QC and metagenomics
  179. Microbial DNA extraction
  180. Resolve species/strain in metagenomic bin
  181. Using prokka in metAmos
  182. Clustering/Binning Metagenomic contigs with MyCC and 16S sequences
  183. auto log-off on IMG website
  184. Question about whole genome metagenomics for the microbiome?
  185. paired end data not aligned in NextSeq 500
  186. Extraction
  187. Culturable microbiome NGS
  188. New metagenomics analysis platform: Nephele
  189. Post binning
  190. MiSeq Micro/Nano Kits v2 for 16S?
  191. 16S triplicates
  192. Spiked-in control for microbiome
  193. Metagenomic DNA/RNA from human tissue samples
  194. EBI Metagenomics: How to analyze NCBI data?
  195. Training in Metagenomics Data Analysis @NIH, USA, Nov 7-10,2016
  196. Multithread MyCC
  197. inconsistency in aligning metagenomic data in Bowtie2
  198. 21,000 Human Microbiome Dataset Collection
  199. Concentrations of Post-indexed libraries
  200. Minimum amount of data needed for reliable results?
  201. MetaSUB Inter-City Challenge - [email protected]/ECCB
  202. megahit failing without an error message in (x)ubuntu virtual machine
  203. Metagenomic survey of gut microbiota - depth, tradeoff and num. of samples to include
  204. Advice on assembling very large metagenomic dataset?
  205. How to extract subregions from Miseq 16srRNA data?
  206. Read lenght in 16S RNA data
  207. how to count the mapped reads with bbmap?
  208. Extraction of genomic DNA from RNAlater preserved cattle tissue Using DNA extraction
  209. What is the best DNA extraction kits for RNAlater preserved cattle tissue
  210. Convert mothur classify.seqs output to BIOM format
  211. Studying soil microbial communities
  212. Same sample different results
  213. Find single copy gene for bacteria and archaea
  214. QIIME vs Mothur vs UPARSE
  215. 16S sequencing tissue - host DNA contamination
  216. Processing a very large soil dataset
  217. Workshop: Metagenomics Analysis with MEGAN6
  218. raw illumina reads or assembled contigs for Taxonomy
  219. Illumina 16s protocol: size
  220. recA database?
  221. Best tool to find gene variants in metagenome data
  222. Normalization for NGS count data with high variance between observations / uneven com
  223. calculate genome bins' similarity
  224. quality filtering error usearch
  225. merge contigs of different K-mers of metagenomic data
  226. Alpha and betadiversity why??
  227. Generate local blast database with RefSeq bacteria AND taxonomy
  228. MetaSUB Forensics Challenge @CAMDA ISMB Chicago
  229. Crowdsourcing the Advancement of Microbiome Research: Mosaic & precisionFDA Challenge
  230. V4-V5 Region Using 2x250 - Enough Overlap?
  231. Simple statistics help
  232. I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but
  233. Sanger Sequencing for Community Analysis
  234. FastQC results for 16s reads